{"entity": "researcher", "timestamp": "2026-07-17T08:33:34.301Z", "family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "affiliations": ["Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 77, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca"}}, "publications": [{"entity": "publication", "iuid": "72f3aa35636c456e84ca5ceb90728c2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3aa35636c456e84ca5ceb90728c2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3aa35636c456e84ca5ceb90728c2a"}}, "title": "Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.", "authors": [{"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ"}, {"family": "Savva", "given": "Christina", "initials": "C"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R"}, {"family": "Shen", "given": "Joanne X", "initials": "JX", "orcid": "0009-0008-0322-5615", "researcher": {"href": "https://publications.scilifelab.se/researcher/519a2d0afb6747c6ad3cf2b12c4d0bf3.json"}}, {"family": "Carravilla", "given": "Pablo", "initials": "P"}, {"family": "Geng", "given": "Keyi", "initials": "K"}, {"family": "N\u00f8rskov S\u00f8ndergaard", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0125f039a4949d8a22b9048d7f6b7d8.json"}}, {"family": "Ferrer-Aumatell", "given": "Cl\u00e0udia", "initials": "C"}, {"family": "Mercier", "given": "Gr\u00e9goire", "initials": "G"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Korach-Andr\u00e9", "given": "Marion", "initials": "M"}, {"family": "Petersson", "given": "Carl", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Hannes", "initials": "H"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C"}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "volume": "20", "issue": "4", "pages": "374-402", "issn-l": "1744-4292"}, "abstract": "Sex-based differences in obesity-related hepatic malignancies suggest the protective roles of estrogen. Using a preclinical model, we dissected estrogen receptor (ER) isoform-driven molecular responses in high-fat diet (HFD)-induced liver diseases of male and female mice treated with or without an estrogen agonist by integrating liver multi-omics data. We found that selective ER activation recovers HFD-induced molecular and physiological liver phenotypes. HFD and systemic ER activation altered core liver pathways, beyond lipid metabolism, that are consistent between mice and primates. By including patient cohort data, we uncovered that ER-regulated enhancers govern central regulatory and metabolic genes with clinical significance in metabolic dysfunction-associated steatotic liver disease (MASLD) patients, including the transcription factor TEAD1. TEAD1 expression increased in MASLD patients, and its downregulation by short interfering RNA reduced intracellular lipid content. Subsequent TEAD small molecule inhibition improved steatosis in primary human hepatocyte spheroids by suppressing lipogenic pathways. Thus, TEAD1 emerged as a new therapeutic candidate whose inhibition ameliorates hepatic steatosis.", "doi": "10.1038/s44320-024-00024-x", "pmid": "38459198", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Integrated Microscopy Technologies Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10987545"}, {"db": "pii", "key": "10.1038/s44320-024-00024-x"}], "notes": [], "created": "2024-03-14T11:08:10.304Z", "modified": "2025-02-28T14:16:38.102Z"}, {"entity": "publication", "iuid": "9548e88f13764743811099768c2ea421", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9548e88f13764743811099768c2ea421.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9548e88f13764743811099768c2ea421"}}, "title": "Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles.", "authors": [{"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0ce637276ce4cb0b81f9f039d261c61.json"}}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Veiga", "given": "Ra\u00fcl G", "initials": "RG", "orcid": "0000-0002-8517-1559", "researcher": {"href": "https://publications.scilifelab.se/researcher/f012c55305964efb9155c1442c204759.json"}}, {"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Epperlein", "given": "Janine", "initials": "J", "orcid": "0000-0002-1595-5411", "researcher": {"href": "https://publications.scilifelab.se/researcher/83adf9175bcf4737b98bb83b3c715254.json"}}, {"family": "Brinkman", "given": "Eva K", "initials": "EK", "orcid": "0000-0003-3120-1174", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3d3152bb82438e96b23d5f0cfc5ae5.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "7", "issue": "2", "issn-l": "2575-1077"}, "abstract": "The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.", "doi": "10.26508/lsa.202302128", "pmid": "37984988", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10662290"}, {"db": "pii", "key": "7/2/e202302128"}], "notes": [], "created": "2023-12-01T13:23:58.904Z", "modified": "2025-02-28T14:23:40.585Z"}, {"entity": "publication", "iuid": "24debc4b98554ac381461a8be3ba5b25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24debc4b98554ac381461a8be3ba5b25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24debc4b98554ac381461a8be3ba5b25"}}, "title": "Estrogen receptor activation remodelsTEAD1gene expression to alleviate nonalcoholic fatty liver disease", "authors": [{"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ", "orcid": "0000-0002-6086-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d80ebf009104cae8aaf56f9ad998c3b.json"}}, {"family": "Savva", "given": "Christina", "initials": "C", "orcid": "0000-0002-8019-1104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4ce68039184f35922fe3dd337f0ced.json"}}, {"family": "Hases", "given": "Linnea", "initials": "L", "orcid": "0000-0001-6741-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb5e09b88e94ab59a6ca9f8c457c5f4.json"}}, {"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Shen", "given": "Joanne X", "initials": "JX", "orcid": "0009-0008-0322-5615", "researcher": {"href": "https://publications.scilifelab.se/researcher/519a2d0afb6747c6ad3cf2b12c4d0bf3.json"}}, {"family": "Carravilla", "given": "Pablo", "initials": "P", "orcid": "0000-0001-6592-7630", "researcher": {"href": "https://publications.scilifelab.se/researcher/b791a8068a724c179b731f0446b1737a.json"}}, {"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0ce637276ce4cb0b81f9f039d261c61.json"}}, {"family": "N\u00f8rskov S\u00f8ndergaard", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0125f039a4949d8a22b9048d7f6b7d8.json"}}, {"family": "Ferrer-Aumatell", "given": "Cl\u00e0udia", "initials": "C", "orcid": "0009-0008-9828-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/a492fadc2d4e41028a5d103a87e214aa.json"}}, {"family": "Mercier", "given": "Gr\u00e9goire", "initials": "G", "orcid": "0009-0002-9966-9910", "researcher": {"href": "https://publications.scilifelab.se/researcher/b363ed8d40cd4bfdae8783c85922036b.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Korach-Andr\u00e9", "given": "Marion", "initials": "M", "orcid": "0000-0003-3292-9124", "researcher": {"href": "https://publications.scilifelab.se/researcher/407729e3f36742a890a54a8bac2e9662.json"}}, {"family": "Petersson", "given": "Carl", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Hannes", "initials": "H", "orcid": "0000-0002-8474-1759", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e5d3927690e4563a049c1703ecc4034.json"}}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "posted-content", "published": "2023-09-08", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.09.07.556687", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-10T11:47:13.965Z", "modified": "2025-12-18T19:46:10.899Z"}, {"entity": "publication", "iuid": "e1303284fb4b4381bf572cddee87b7c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1303284fb4b4381bf572cddee87b7c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1303284fb4b4381bf572cddee87b7c5"}}, "title": "Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.", "authors": [{"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0ce637276ce4cb0b81f9f039d261c61.json"}}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Wedemann", "given": "Linda", "initials": "L", "orcid": "0000-0003-1096-9037", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd521e37844343ceb57f0982c00f96e0.json"}}, {"family": "Martens", "given": "Aniek", "initials": "A", "orcid": "0000-0002-0291-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a95bab270846d4aa1c2acaaa7dd270.json"}}, {"family": "Sobota", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Sanchez", "given": "Yerma P", "initials": "YP", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications.scilifelab.se/researcher/856bd810312b4ccab13131df5f6bf02c.json"}}, {"family": "S\u00f8ndergaard", "given": "Jonas N\u00f8rskov", "initials": "JN", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0125f039a4949d8a22b9048d7f6b7d8.json"}}, {"family": "White", "given": "Robert J", "initials": "RJ", "orcid": "0000-0002-9631-7760", "researcher": {"href": "https://publications.scilifelab.se/researcher/10bee055303944cba821141ea9593777.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "32", "issue": "10", "pages": "1876-1891", "issn-l": "1088-9051"}, "abstract": "The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.", "doi": "10.1101/gr.276901.122", "pmid": "36180232", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9712622"}, {"db": "pii", "key": "gr.276901.122"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-11-27T21:55:28.786Z", "modified": "2024-01-16T13:48:34.825Z"}, {"entity": "publication", "iuid": "6af623400b4f427b8dd9acefb977543a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6af623400b4f427b8dd9acefb977543a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6af623400b4f427b8dd9acefb977543a"}}, "title": "Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.", "authors": [{"family": "Gao", "given": "William", "initials": "W", "orcid": "0000-0002-9415-331X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d774b12db3942399c882dea6be4b733.json"}}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ", "orcid": "0000-0002-6086-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d80ebf009104cae8aaf56f9ad998c3b.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "32", "issue": "1", "pages": "97-110", "issn-l": "1088-9051"}, "abstract": "The correlation between codon and anticodon pools influences the efficiency of translation, but whether differences exist in these pools across individual cells is unknown. We determined that codon usage and amino acid demand are highly stable across different cell types using available mouse and human single-cell RNA-sequencing atlases. After showing the robustness of ATAC-sequencing measurements for the analysis of tRNA gene usage, we quantified anticodon usage and amino acid supply in both mouse and human single-cell ATAC-seq atlases. We found that tRNA gene usage is overall coordinated across cell types, except in neurons, which clustered separately from other cell types. Integration of these data sets revealed a strong and statistically significant correlation between amino acid supply and demand across almost all cell types. Neurons have an enhanced translation efficiency over other cell types, driven by an increased supply of tRNAAla (AGC) anticodons. This results in faster decoding of the Ala-GCC codon, as determined by cell type-specific ribosome profiling, suggesting that the reduction of tRNAAla (AGC) anticodon pools may be implicated in neurological pathologies. This study, the first such examination of codon usage, anticodon usage, and translation efficiency resolved at the cell-type level with single-cell information, identifies a conserved landscape of translation elongation across mammalian cellular diversity and evolution.", "doi": "10.1101/gr.275944.121", "pmid": "34857654", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8744671"}, {"db": "pii", "key": "gr.275944.121"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-11-27T21:55:23.280Z", "modified": "2024-01-16T13:48:37.945Z"}]}